bmtk.utils package#

Subpackages#

Submodules#

bmtk.utils.hdf5_helper module#

bmtk.utils.hdf5_helper.get_attribute_h5(h5obj, attribut_name, default=None)[source]#

bmtk.utils.lazy_property module#

bmtk.utils.lazy_property.lazy_property(fn)[source]#

bmtk.utils.sim_setup module#

class bmtk.utils.sim_setup.BioNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]#

Bases: EnvBuilder

property bmtk_simulator#
compile_mechanisms()[source]#
property examples_dir#
property target_simulator#
class bmtk.utils.sim_setup.EnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]#

Bases: object

property base_dir#
property bmtk_simulator#
build(include_examples=False, use_relative_paths=True, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, config_file='config.json', overwrite_config=False, **run_args)[source]#
property components_dir#
property examples_dir#
property network_dir#
property node_sets_file#
property output_dir#
property scripts_root#
property target_simulator#
class bmtk.utils.sim_setup.FilterNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]#

Bases: EnvBuilder

property bmtk_simulator#
property examples_dir#
property target_simulator#
class bmtk.utils.sim_setup.PointNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]#

Bases: EnvBuilder

property bmtk_simulator#
property examples_dir#
property target_simulator#
class bmtk.utils.sim_setup.PopNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]#

Bases: EnvBuilder

property bmtk_simulator#
property examples_dir#
property target_simulator#
bmtk.utils.sim_setup.build_env_bionet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, overwrite_config=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=-15.0, nsteps_block=5000, v_init=-80.0, celsius=34.0, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, compile_mechanisms=False, use_relative_paths=True, config_file=None)[source]#
bmtk.utils.sim_setup.build_env_filternet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, config_file='config.json')[source]#
bmtk.utils.sim_setup.build_env_pointnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, overwrite_config=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=-15.0, nsteps_block=5000, v_init=-80.0, celsius=34.0, report_vars=[], report_nodes=None, current_clamp=None, spikes_inputs=None, use_relative_paths=True, config_file=None)[source]#
bmtk.utils.sim_setup.build_env_popnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, reports=None, include_examples=True, config_file=None, tstart=0.0, tstop=1000.0, dt=0.001, **args)[source]#

Module contents#